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P30820 (NIGY_DESVH) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 97. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Nigerythrin
Gene names
Name:ngr
Ordered Locus Names:DVU_0019
OrganismDesulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303) [Reference proteome] [HAMAP]
Taxonomic identifier882 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Deltaproteobacteria › Desulfovibrionales › Desulfovibrionaceae › Desulfovibrio ›

Protein attributes

Sequence length202 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Exhibits NADH peroxidase activity (in vitro).

Subunit structure

Homodimer. May possess two rubredoxin-like centers and two hemerythrin-like binuclear-iron centers per dimer.

Subcellular location

Cytoplasm Probable.

Sequence similarities

Contains 1 ferritin-like diiron domain.

Contains 1 rubredoxin-like domain.

Ontologies

Keywords
   Biological processElectron transport
Transport
   Cellular componentCytoplasm
   LigandIron
Metal-binding
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processelectron transport chain

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functioniron ion binding

Inferred from electronic annotation. Source: InterPro

oxidoreductase activity

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 202202Nigerythrin
PRO_0000135072

Regions

Domain23 – 168146Ferritin-like diiron
Domain169 – 20234Rubredoxin-like

Sites

Metal binding401Iron 1
Metal binding731Iron 1
Metal binding731Iron 2
Metal binding1151Iron 2
Metal binding1181Iron 1
Metal binding1491Iron 1
Metal binding1491Iron 2
Metal binding1521Iron 2
Metal binding1741Iron 3
Metal binding1771Iron 3
Metal binding1891Iron 3
Metal binding1921Iron 3

Experimental info

Sequence conflict1291K → E in AAC45480. Ref.1
Sequence conflict1321E → G in AAC45480. Ref.1

Secondary structure

1 ......................... 202
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P30820 [UniParc].

Last modified May 24, 2004. Version 3.
Checksum: DF5410519EE8D899

FASTA20222,098
        10         20         30         40         50         60 
MKVRAQVPTV KNATNFNMVA DSKTAVGSTL ENLKAAIAGE TGAHAKYTAF AKAAREQGYE 

        70         80         90        100        110        120 
QIARLFEATA AAELIHIGLE YALVAEMEPG YEKPTVAAPS AYSCDLNLIS GANGEIYETS 

       130        140        150        160        170        180 
DMYPAFIRKA QEEGNSKAVH VFTRAKLAES VHAERYLAAY NDIDAPDDDK FHLCPICGYI 

       190        200 
HKGEDFEKCP ICFRPKDTFT AY

« Hide

References

« Hide 'large scale' references
[1]"A rubrerythrin operon and nigerythrin gene in Desulfovibrio vulgaris (Hildenborough)."
Lumppio H.L., Shenvi N.V., Garg R.P., Summers A.O., Kurtz D.M. Jr.
J. Bacteriol. 179:4607-4615(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough."
Heidelberg J.F., Seshadri R., Haveman S.A., Hemme C.L., Paulsen I.T., Kolonay J.F., Eisen J.A., Ward N.L., Methe B.A., Brinkac L.M., Daugherty S.C., DeBoy R.T., Dodson R.J., Durkin A.S., Madupu R., Nelson W.C., Sullivan S.A., Fouts D.E. expand/collapse author list , Haft D.H., Selengut J., Peterson J.D., Davidsen T.M., Zafar N., Zhou L., Radune D., Dimitrov G., Hance M., Tran K., Khouri H.M., Gill J., Utterback T.R., Feldblyum T.V., Wall J.D., Voordouw G., Fraser C.M.
Nat. Biotechnol. 22:554-559(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: Hildenborough / ATCC 29579 / NCIMB 8303.
[3]"Nigerythrin and rubrerythrin from Desulfovibrio vulgaris each contain two mononuclear iron centers and two dinuclear iron clusters."
Pierik A.J., Wolbert R.B.G., Portier G.L., Verhagen M.F.J.M., Hagen W.R.
Eur. J. Biochem. 212:237-245(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 1-15.
[4]"High-resolution crystal structures of Desulfovibrio vulgaris (Hildenborough) nigerythrin: facile, redox-dependent iron movement, domain interface variability, and peroxidase activity in the rubrerythrins."
Iyer R.B., Silaghi-Dumitrescu R., Kurtz D.M. Jr., Lanzilotta W.N.
J. Biol. Inorg. Chem. 10:407-416(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS), IRON-BINDING SITES.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		U71215 Genomic DNA. Translation: AAC45480.1.
AE017285 Genomic DNA. Translation: AAS94503.1.
RefSeqYP_009244.1. NC_002937.3.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1YUXX-ray1.60A/B1-202[»]
1YUZX-ray1.40A/B1-202[»]
1YV1X-ray1.50A/B1-202[»]
ProteinModelPortalP30820.
SMRP30820. Positions 1-202.
ModBaseSearch...

Protein-protein interaction databases

STRING882.DVU0019.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAS94503; AAS94503; DVU_0019.
GeneID2794280.
KEGGdvu:DVU0019.
PATRIC32060008. VBIDesVul119526_0016.

Phylogenomic databases

eggNOGCOG1592.
OMAITFTHAM.
ProtClustDBCLSK704352.

Enzyme and pathway databases

BioCycDVUL882:GJIL-20-MONOMER.

Family and domain databases

Gene3D1.20.1260.10. 1 hit.
2.20.28.10. 1 hit.
InterProIPR009040. Ferritin-like_diiron.
IPR009078. Ferritin-like_SF.
IPR012347. Ferritin-rel.
IPR024934. Rubredoxin-like_dom.
IPR004039. Rubredoxin-type_fold.
IPR003251. Rubrerythrin.
[Graphical view]
PfamPF02915. Rubrerythrin. 1 hit.
[Graphical view]
SUPFAMSSF47240. Ferritin/RR_like. 1 hit.
PROSITEPS50905. FERRITIN_LIKE. 1 hit.
PS50903. RUBREDOXIN_LIKE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP30820.

Entry information

Entry nameNIGY_DESVH
AccessionPrimary (citable) accession number: P30820
Entry history
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: May 24, 2004
Last modified: May 1, 2013
This is version 97 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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